Python for Biologists
Programming for Scientific Computing
Python is a flexible programming language that is becoming increasingly popular for scientific computing. This course will give you a basic introduciton in how to use Python. The course will work towards a script for parsing FASTA files and calculating the GC-content of DNA sequences.
Instructors
- Tjelvar Olsson
- Matthew Hartley
Audience
For beginners interested in using Python to solve problems in Biology.
Overview
Python is a flexible programming language that is becoming increasingly popular for scientific computing. The course is is split into 12 modules and runs over two half days. At the end of each module there a number of exercises to help solidify the learning. By the end of day one you will have created a function for calculating the GC-content of DNA sequences. By the end of day two you will have a script for reading in sequences from FASTA files. The final exercise will be two combine the two to create a script that can read a FASTA file and calculate the GC-content of each sequence in that file.
Schedule
Day 1
9:30 Start
11:00 Coffee break
13:00 End
Day 2
9:30 Start
11:00 Coffee break
13:00 End
Learning outcomes
By the end of the course you should be able to:
- Ability to run Python scripts and work in interactive Python sessions
- Ability to understand and edit existing Python scripts
- Ability to manipulate numbers and text
- Ability to create reusable functions
- Basic understanding of Python's built-in data types and structures
- Basic understanding of control flow and loops
- Ability to read in and write out files
- Ability to reuse functionality from Python's built-in standard library
- Experience of creating a complex data analysis script
Pre-requisites
No previous experience is needed although some basic familiarity with programming and/or the Linux command line would be beneficial. As the course is structured around the participants working through course material a certain degree of curiosity and self motivation is required along with a willingness to ask for help and clarification when required.
Full course syllabus
- Interacting with Python
- Editing scripts
- Manipulating numbers
- Manipulating strings
- Creating reusable functions
- Data types
- Data structures
- Control flow and loops
- Reading and writing files
- Reusing code
- Parsing FASTA files
- Linking it all together
- Further reading
Course materials
Course book
Programming for Scientific Computing
Instructors
- Tjelvar Olsson
- Matthew Hartley
Audience
For beginners interested in using Python to solve problems in Biology.Overview
Python is a flexible programming language that is becoming increasingly popular for scientific computing. The course is is split into 12 modules and runs over two half days. At the end of each module there a number of exercises to help solidify the learning. By the end of day one you will have created a function for calculating the GC-content of DNA sequences. By the end of day two you will have a script for reading in sequences from FASTA files. The final exercise will be two combine the two to create a script that can read a FASTA file and calculate the GC-content of each sequence in that file.Schedule
Day 1
| 9:30 | Start |
| 11:00 | Coffee break |
| 13:00 | End |
Day 2
| 9:30 | Start |
| 11:00 | Coffee break |
| 13:00 | End |
Learning outcomes
By the end of the course you should be able to:- Ability to run Python scripts and work in interactive Python sessions
- Ability to understand and edit existing Python scripts
- Ability to manipulate numbers and text
- Ability to create reusable functions
- Basic understanding of Python's built-in data types and structures
- Basic understanding of control flow and loops
- Ability to read in and write out files
- Ability to reuse functionality from Python's built-in standard library
- Experience of creating a complex data analysis script
Pre-requisites
No previous experience is needed although some basic familiarity with programming and/or the Linux command line would be beneficial. As the course is structured around the participants working through course material a certain degree of curiosity and self motivation is required along with a willingness to ask for help and clarification when required.Full course syllabus
- Interacting with Python
- Editing scripts
- Manipulating numbers
- Manipulating strings
- Creating reusable functions
- Data types
- Data structures
- Control flow and loops
- Reading and writing files
- Reusing code
- Parsing FASTA files
- Linking it all together
- Further reading